 1998 Oxford University Press
Nucleic Acids Research, 1998, Vol. 26, No. 1
351–352
The Ribonuclease P Database
James W. Brown
Department of Microbiology, North Carolina State University, Raleigh, NC 27695, USA
Received September 25, 1997; Accepted September 26, 1997
ABSTRACT
Ribonuclease P is responsible for the 5′-maturation of
tRNA precursors. Ribonuclease P is a ribonucleoprotein, and in bacteria the RNA subunit alone is
catalytically active in vitro, i.e., it is a ribozyme. The
Ribonuclease P Database is a compilation of ribonuclease P sequences, sequence alignments,
secondary structures, three-dimensional models, and
accessory information, available via the World Wide
Web (http://www.mbio.ncsu.edu/RNaseP/home.html ).
INTRODUCTION
Ribonuclease P is the ribonucleoprotein endonuclease that
cleaves transfer RNA precursors, removing 5′ precursor
sequences and generating the mature 5′ terminus of the tRNA (see
ref. 1 for a review). RNase P is also implicated in the processing
of other RNA precursors. In bacteria, in which RNase P is best
understood, the holoenzyme consists of two subunits, an RNA of
∼400 nt and a protein of ∼120 amino acids (2). The RNA is the
catalytic subunit of the enzyme; the bacterial RNase P RNA
subunit alone is catalytically proficient, at high ionic strength in
vitro (3). In the last few years, the number and diversity of RNase
P RNA sequences available has increased dramatically.
On a yearly basis since 1991, RNase P RNA sequence
alignments and secondary structures have been compiled and
distributed in an informal publication, ‘The Book of P’, providing
a single source for comparative information. In 1994 the
Ribonuclease P Sequence Database was established as an
electronic means of distributing the Book of P and in its eighth
release (described here) is a well-established and widely-used
World Wide Web resource.
DESCRIPTION
The Ribonuclease P Sequence Database is a compilation of
RNase P sequences, sequence alignments, secondary structures,
three-dimensional models, and accessory information available
electronically via the World Wide Web (Fig. 1 see below for
details on accessing the database). The hypertext format of the
database makes access to its various components straightforward.
The database primarily contains information on bacterial and
archaeal RNase P, focusing on the RNA subunit of the enzyme,
although information is also included on the eucaryal and
organellar RNase P RNAs and proteins. The database is updated
Tel: +1 919 515 8803; Fax: +1 919 515 7867; Email: jwbrown@mbio.ncsu.edu
as additional sequences and structural information becomes
available.
The RNase P RNA and protein sequences in the database are
available from lists arranged phylogenetically as individual
sequences or as alignments in GenBank format. Secondary
structures of each RNA are presented in Graphic Interchange
Format (GIFs) and can be downloaded either as level 1 Postscript
(.ps) or Adobe Acrobat (.pdf) files. Models of the threedimensional structure of the RNA are provided in Protein
Database (PDB) format and as Quicktime movies. Accessory
information, such as reference structures, phylogenetic trees,
computer programs, and reference listings are also made
available as part of the database.
AVAILABLITY
The Ribonuclease P Database is accessible using any World Wide
Web browser (e.g., Netscape Navigator, Microsoft Explorer) at
the URL http://www.mbio.ncsu.edu/RNaseP/home.html . A
CD-ROM copy of the RNase P Database is available for those
without access to the World Wide Web. The administrator of the
Ribonuclease P database (JWB) can be contacted by electronic
mail (jwbrown@mbio.ncsu.edu) or by mail at the address given
above. Users of the Ribonuclease P Database should cite this
publication.
PLEA FOR HELP
Users of the Ribonuclease P database are encouraged to provide
corrections, new information, or other materials for inclusion in
the database; unpublished information will be held confidential
(via username and password protection) at the author’s request.
Help is especially needed for expansion of the data made
available on the eukaryotic RNase P enzymes.
ACKNOWLEDGEMENT
Research on RNase P in the author’s laboratory is supported by
NIH grant GM52894.
REFERENCES
1 Pace,N.R. and Brown,J.W. (1995) J. Bacteriol., 177, 1919–1928.
2 Brown,J.W. and Pace,N.R. (1992) Nucleic Acids Res., 20, 1451–1456.
3 Guerrier-Takada,C., Gardiner,K., Marsh,T., Pace,N. and Altman,S. (1983)
Cell, 35, 849–857.
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Nucleic Acids Research, 1998, Vol. 26, No. 1
Figure 1. The Ribonuclease P Database home page. The appearence of the Ribonuclease P Database home page is shown as it appears in graphics-capable World
Wide Web browser (Netscape Navigator, in this case). Links to the various sections of the Ribonuclease P Database are shown in blue.